Hi Salmon
Yes, that is correct. Upload it to public_html or any subdirectory that you want those settings to apply to.
If you want it to work for the entire site, you can do this:
Add the following line to the .htaccess file:
suPHP_ConfigPath /home/cpuser/path/to/php.ini
Then the php.ini will be used by all of that account's scripts / subdirs by default.
It prevents the need for many php.ini files.